Sequence is char []

[jalview.git] / src / jalview / schemes / ClustalxColourScheme.java

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 4c20873..eaf2a5f 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -70,23 +70,23 @@ public class ClustalxColourScheme
     int res;\r
     int i;\r
     int j = 0;\r
-    String seq;\r
+    char [] seq;\r
 \r
     while (j < seqs.size())\r
     {\r
       seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
 \r
-      int end_j = seq.length() - 1;\r
+      int end_j = seq.length - 1;\r
 \r
       for (i = start; i <= end_j; i++)\r
       {\r
-        if ( (seq.length() - 1) < i)\r
+        if ( (seq.length - 1) < i)\r
         {\r
           res = 23;\r
         }\r
         else\r
         {\r
-          res =  ResidueProperties.aaIndex[seq.charAt(i)];\r
+          res =  ResidueProperties.aaIndex[seq[i]];\r
         }\r
 \r
         cons2[i][res]++;\r
@@ -240,22 +240,22 @@ public class ClustalxColourScheme
     ResidueColour[19] = colours[0]; // V\r
   }\r
 \r
-  public Color findColour(String s)\r
+  public Color findColour(char c)\r
   {\r
     return Color.pink;\r
   }\r
 \r
-  public Color findColour(String s, int j)\r
+  public Color findColour(char c, int j)\r
   {\r
     Color currentColour;\r
 \r
 \r
-    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j)))\r
+    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))\r
     {\r
       return Color.white;\r
     }\r
 \r
-    int i = ResidueProperties.aaIndex[s.charAt(0)];\r
+    int i = ResidueProperties.aaIndex[c];\r
 \r
     currentColour = Color.white;\r
 \r